Variant report

Variant	rs71477720
Chromosome Location	chr11:71954487-71954488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:71944622-71955431	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr11:71953907-71954914	SK-N-SH	brain:	n/a	n/a
3	GATA2	chr11:71954162-71954762	SH-SY5Y	brain:	n/a	chr11:71954448-71954465 chr11:71954444-71954453 chr11:71954467-71954476
4	REST	chr11:71954192-71954490	SK-N-SH	brain:	n/a	chr11:71954392-71954412 chr11:71954396-71954409 chr11:71954393-71954411
5	MXI1	chr11:71953931-71956605	SK-N-SH	brain:	n/a	n/a
6	RAD21	chr11:71954283-71954860	SK-N-SH_RA	brain:	n/a	n/a
7	EP300	chr11:71953915-71957050	SK-N-SH	brain:	n/a	chr11:71956843-71956856

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:71951601..71953593-chr11:71954198..71956638,2	K562	blood:
2	chr11:71948375..71952014-chr11:71952052..71958381,8	MCF-7	breast:

Variant related genes	Relation type
PHOX2A	TF binding region
ENSG00000165458	Chromatin interaction
ENSG00000165462	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12807696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34116110	1.00[AMR][1000 genomes]
rs34575766	1.00[AFR][1000 genomes]
rs34738484	1.00[AMR][1000 genomes]
rs35437876	1.00[AFR][1000 genomes]
rs71477715	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv897908	chr11:71927468-71956890	ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897909	chr11:71927468-71960554	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv3326211	chr11:71953829-71956677	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71952400-71954800	Weak transcription	Gastric	stomach
2	chr11:71952400-71955400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
3	chr11:71953000-71956000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr11:71954000-71954600	Bivalent/Poised TSS	Fetal Intestine Small	intestine
5	chr11:71954000-71954800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
6	chr11:71954000-71956800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr11:71954200-71954600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:71954200-71955000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr11:71954200-71955200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr11:71954200-71955800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr11:71954200-71956200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:71954400-71954600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:71954400-71954600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:71954400-71954600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr11:71954400-71954600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr11:71954400-71954600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
17	chr11:71954400-71954800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
18	chr11:71954400-71954800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
19	chr11:71954400-71954800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:71954400-71955400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:71954400-71955600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:71954400-71955800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr11:71954400-71955800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr11:71954400-71955800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
25	chr11:71954400-71955800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:71954400-71956800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
27	chr11:71954400-71957000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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